Mutations in the breast cancer susceptibility gene BRCA1 predispose individuals to breast and ovarian cancers. Cofactor of BRCA1 (COBRA1), a novel protein, was isolated as a BRCA1-interacting protein. However, the role of COBRA1 in breast cancer is poorly understood. In this study, we demonstrate that COBRA1 mRNA was differentially expressed in breast cancer cell lines by semi-quantitative reverse transcription-polymerase chain PCR (RT-PCR). We developed a highly specific rabbit polyclonal anti-COBRA1 antibody using GST-COBRA1 fusion protein. In most cases, the levels of COBRA1 protein in breast cancer cell lines detected by Western blotting with the anti-COBRA1 antibody correlated with those of COBRA1 mRNA. Immunofluorescence analysis indicated that COBRA1 was a nuclear protein. Endogenously expressed COBRA1 interacted with the nuclear protein BRCA1 in human breast cancer cells. These data suggest that the COBRA1 antibody may be a useful tool to investigate functions of COBRA1 in cancers and that, like BRCA1, COBRA1 may regulate various nuclear events in breast cancer cells.